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Comment: C: interaction models DESeq2
5.6 years ago aec ▴ 90
1
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3
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1.5k
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interaction models DESeq2
deseq2 interaction model
updated 5.6 years ago by 43k • written 5.6 years ago by ▴ 90
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0
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5.7k
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Comment: C: removing genes before RNA-seq normalization
6.2 years ago aec ▴ 90
2
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6
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5.7k
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removing genes before RNA-seq normalization
edger deseq2 normalization removing genes
updated 3.7 years ago by 53k • written 6.2 years ago by ▴ 90
8
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4
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3.5k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin edgeR deseq2 normalization rnaseq
updated 6.9 years ago by ★ 7.9k • written 6.9 years ago by ▴ 90
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Comment: C: edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
6.9 years ago aec ▴ 90
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0
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3.6k
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Comment: C: time series, block by patient, between and within comparisons limma-voom
7.3 years ago aec ▴ 90
2
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8
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3.6k
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time series, block by patient, between and within comparisons limma-voom
rna-seq time series patient limma-voom
updated 7.3 years ago by ★ 29k • written 7.3 years ago by ▴ 90
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3.6k
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Comment: C: time series, block by patient, between and within comparisons limma-voom
7.3 years ago aec ▴ 90
0
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1
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3.6k
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Comment: C: time series, block by patient, between and within comparisons limma-voom
7.3 years ago aec ▴ 90
0
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0
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3.6k
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Comment: C: time series, block by patient, between and within comparisons limma-voom
7.3 years ago aec ▴ 90
0
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1
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1.1k
views
question about "write.fit" function in limma-voom
limma write.fit method nestedF
updated 7.7 years ago by 53k • written 8.2 years ago by ▴ 90
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0
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1.9k
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
7.7 years ago aec ▴ 90
0
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1
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1.9k
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
7.7 years ago aec ▴ 90
0
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1
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1.9k
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Comment: C: differential expression analysis with big dataset and >500 surrogate variables
7.7 years ago aec ▴ 90
1
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6
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1.9k
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differential expression analysis with big dataset and >500 surrogate variables
SVA deseq2 differential expression LRT
7.7 years ago aec ▴ 90
0
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1
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1.3k
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Comment: C: interaction model deseq2 specific DE genes
7.7 years ago aec ▴ 90
0
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3
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1.3k
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interaction model deseq2 specific DE genes
deseq2 interaction model differential expression
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 90
0
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0
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2.1k
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Comment: C: weird behaviour DESeq2 1.18.1
7.9 years ago aec ▴ 90
0
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1
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2.1k
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Comment: C: weird behaviour DESeq2 1.18.1
7.9 years ago aec ▴ 90
0
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1
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2.1k
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Comment: C: weird behaviour DESeq2 1.18.1
7.9 years ago aec ▴ 90
0
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6
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2.1k
views
weird behaviour DESeq2 1.18.1
deseq2 outliers version
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 90
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0
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2.0k
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Comment: C: significant genes with DESeq2 plenty of outliers and zero counts
7.9 years ago aec ▴ 90
0
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1
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2.0k
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Comment: C: significant genes with DESeq2 plenty of outliers and zero counts
7.9 years ago aec ▴ 90
0
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4
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2.0k
views
significant genes with DESeq2 plenty of outliers and zero counts
zero counts deseq2 odd results outliers
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 90
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1
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1.9k
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Comment: C: disagreement between log2FoldChange and lfcMLE in DESeq2
8.1 years ago aec ▴ 90
0
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3
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1.9k
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disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2 log2fc shrinkage
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 90
0
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0
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3.3k
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Comment: C: Applying sva is compatible with limma duplicateCorrelation?
8.5 years ago aec ▴ 90
0
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0
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3.0k
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Comment: C: normalization affects drastically limma-voom + sva results
8.5 years ago aec ▴ 90
0
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1
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3.0k
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Comment: C: normalization affects drastically limma-voom + sva results
8.5 years ago aec ▴ 90
0
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1
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3.0k
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Comment: C: normalization affects drastically limma-voom + sva results
8.5 years ago aec ▴ 90
1
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6
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3.0k
views
normalization affects drastically limma-voom + sva results
normalization sva limma-voom
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 90
0
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1
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3.3k
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Comment: C: Applying sva is compatible with limma duplicateCorrelation?
8.5 years ago aec ▴ 90
0
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7
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3.3k
views
Applying sva is compatible with limma duplicateCorrelation?
limma-voom sva duplicatecorrelation
updated 8.5 years ago by ▴ 130 • written 8.5 years ago by ▴ 90
0
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0
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2.8k
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Comment: C: How to adjust for different cell type mixtures in differential expression analys
8.5 years ago aec ▴ 90
1
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2
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2.8k
views
How to adjust for different cell type mixtures in differential expression analysis?
cell types differential expression adjustment mixtures rnaseq
updated 8.5 years ago by ★ 7.9k • written 8.5 years ago by ▴ 90
0
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1
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1.7k
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 90
2
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0
replies
909
views
differential expression with heterogenous disease
heterogenous differential expression individual effects
8.8 years ago aec ▴ 90
0
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1
reply
3.2k
views
Comment: C: How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
8.8 years ago aec ▴ 90
2
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3
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3.2k
views
How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression TMM normalization rnaseq edger
8.8 years ago aec ▴ 90
0
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0
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2.6k
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Comment: C: How to proceed with different degradation levels of RNA-seq samples?
8.8 years ago aec ▴ 90
1
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2
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2.6k
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How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 90
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0
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2.0k
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Comment: C: How different ploidy affect differential expression analysis with RNA-seq
8.8 years ago aec ▴ 90
1
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3
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2.0k
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How different ploidy affect differential expression analysis with RNA-seq
ploidy normalization rna-seq differential expression assumption
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 90
0
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0
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2.0k
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Comment: C: edgeR time series DMSO correction
9.2 years ago aec ▴ 90
0
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1
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2.0k
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Comment: C: edgeR time series DMSO correction
9.2 years ago aec ▴ 90
0
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1
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2.0k
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Comment: C: edgeR time series DMSO correction
9.2 years ago aec ▴ 90
1
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6
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2.0k
views
edgeR time series DMSO correction
edger makecontrasts timecourse
updated 9.2 years ago by ★ 7.9k • written 9.2 years ago by ▴ 90
3
votes
6
replies
1.7k
views
Paired RNA-seq experiment with 3 factors using duplicateCorrelation
paired samples multiple factor design limma voom
updated 9.2 years ago by 53k • written 9.2 years ago by ▴ 90
0
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1
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1.7k
views
Comment: C: Paired RNA-seq experiment with 3 factors using duplicateCorrelation
9.2 years ago aec ▴ 90
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